Always another option
by Ciroth
Summary: The options presented at the end of ME3 failed to give the fans with the ending that made them happy. My take. Possible multi-chapter. Rated for Language. Female Shepard and Traynor.


A/N While I have not touched my other works in some time, I have been playing Mass Effect 3 over the last few days and I will be playing the other two shortly, so forgive me if I mess some things up. All I have to go on is ME3 and the bits of history I found there. I am playing though the other two, might change things as I play but, probably wont. Now, I was not very happy with the ending like many I have seen on this site, so I am writing my own storyline using ME3 as a framework. I am writing Shepard as I see the character, so if some don't feel like I am writing to cannon, feel free to message me but again, this is FanFiction. This will be a Female Shepard and a Samantha Traynor pairing. There might be hints of prior relationships that might crop up. I am not giving any idea as to update timelines as I haven't had a chance to work on my other two fictions in quite some time, but maybe this will kick start me in to working on them again. Oh, and I don't own ME3, Bioware does. Also, this is unbeta'd

A/N2 So...just a few minor changes. If you have read this, only adjusted some of the names, calling creatures by their name. Flushed out Samantha talking about Horizon after playing ME2.

Shepard let water pool in her hands from the sink, her eyes not wanting to look at the mirror, almost afraid of the haunt that would look back at her. She brought the water up to her face, letting the coolness wake her up. Water dripped from her short red hair. She couldn't shake the feeling that she had, of how it all was going to end in a few hours, one way or another. The Normandy was almost at Earth for what was likely the last time.

"Another nightmare love?" a soft voice asked from the bedroom. Shepard shut off the water, and after grabbing a towel to dry her hands, let herself lean on the bathroom door frame. She let her teal eyes look over the woman that shared her bed. "It is the same one I have been having since the Reapers attacked Earth. It is always that little boy that ran from me. I keep seeing him burning, but this time, I saw myself burning." She placed the towel on the counter top and let her nude frame return to the bed. After sitting on the edge of the bed, she let her hand stroke the soft cheek of Samantha Traynor. "I could not save him and I don't know if I am strong enough to save Earth…to save you…" She said the last words in a meager whisper.

"Alliana, you are a strong woman. You have an inner will that would never let them win, even if you have to cheat to do so." Trayner said with a soft chuckle. She sat up and let her arms wrap around the woman she loved. "You couldn't even let a little thing like death stop you, even if you were only mostly dead."

Alliana Shepard looked at her lover. "You heard about that?" She asked

Samantha nodded before kissing Alliana's check. "Well, I didn't believe when they said that you almost died. When you came back from the Cerberus station you looked pretty shook up, so I asked EDI about what happened. She told me about the recording you saw." She kissed Alliana's forehead "I for one am glad you are one stubborn ass."

Alliana shook her head slightly "You got that right."

"Damn right I am Commander..." Samantha started to say when Joker cut in over the intercom "Sorry to wake you Commander but we will be arrive at Earth in 30 minutes." Alliana hit the button to activate the intercom "Be right down." She stood up to get dressed in her battle armor. "Duty calls my love."

Samantha sighed softly as she started to get dressed. "Remember…white picket fence and two kids. You better come home to me Commander. That is an order." Alliana smiled "That is one order I will do everything I can do follow." She said as she finished latching her combat boots. She left her quarters, remembering how she met the woman in her life.

******Day 0 after invasion, in transit to the Citadel******

Alliana stepped into the lift to the bridge, several strands of hair sticking to her cheek and to the back of her neck. A few beads of sweat still rested on her forehead from the intense firefight she just returned from on Mars. She had just returned from picking up Liara on Mars. "Fucking Cerberus." She snarled to herself as she pushed on the railing that wrapped around the lift. "What the hell were they thinking?" She asked herself as the lift doors opened, allowing her to step into the Combat Information Center.

She knew that Joker had the ship on its way to the Mass Relay Station to take the ship to the Citadel and she could catch up with the man shortly. Her eyes fell upon a woman standing at a terminal next to a holographic representation of the galaxy. The woman's shoulder length black hair was cascading over her face as she worked. She turned her head slightly as she heard the lift close. Sapping to attention she turned and stated "Specialist Samantha Traynor Ma'am." She lifted her hand up in a salute. "Communications Officer assigned to you while you are on the SR2 Normandy."

Alliana paused as she walked up to the woman. Her eyes looked over the Specialist, almost as if sizing her ability to be effective, however, something else inside of her stirred. She did not have time to even explore those thoughts at the moment. "Report Specialist" Alliana said in a slightly gravelly voice, strained from the Reaper attack on Earth and the fight she just completed to save the lift of one of her friends.

"Ma'am, you can direct the Normandy from the map in front of you, allowing you tactical displays of the Galaxy in real time. Updates as to who controls each system is also displayed. To the left of the station is a private terminal for your access, where you can observe clips from the ANN that I felt you should see, e-mail, and other issues you might need to complete." Samantha said.

"Thank you Specialist. If that is all" Alliana said, almost not wanting to tear her eyes away from Traynor.

"Yes Commander. If you need anything, please feel free to speak with me." Samantha said, her lips curling at the edges in a slight smile.

Alliana turned to finish the tour of the overhauled Normandy. 'If only she was an officer...' Alliana thought to herself, her mind only half on the tour.

****Day 589 after invasion above Earth, Sol System****

Alliana placed her sniper rifle to her shoulder, letting her eye focus though the scope. A Marauder screwed up skull was within her sights. Taking a slow breath, she held it and squeezed the trigger. With slight satisfaction, she watched the creature's head explode. She pulled the bolt back and realized with a snarl that she was out of ammunition in the rifle. Quickly she shouldered the file and pulled the sub machine gun from behind her back. "Samantha, I am sorry." She whispered "I don't think I am going to make it home." Her heart felt heavy as she squeezed the trigger of her weapon, leaping over a crate that she had used as cover. She winced as she ran for the door, adjusting her feet as she ran to regain her balance as felt her left bicep take the impact of a shot. The weakened armor had allowed some of the blast to sear her arm.

As she slid though a door way, her sub machine gun clicks as it emptied the last round from the chamber. She heard grunting near her, her body snapping her feet as she saw a line of husks between her and the beam to take her to the citadel, the one place where she did not want to be but yet, she had to be. "There is no way in hell I am going to let you fucking zombies get between me and that door." She said. With a snap of her left arm and her hand forming a fist, her hand glowed red, a blade forming in her palm. She formed both her hands into fists, her lips turning into snarl, exposing her teeth.

She let her self drop to one knee as she started to glow blue, her bionics powering up in preparation for a power assisted charge. With a blast of power, Alliana felt herself being propelled across the deck, impacting several Husks, causing them to fly though the air and taking a few more with them. As she turned to sever the head of another, she felt one grab her shoulder with both hands and sink its teeth into her flesh. She let her left hand come up and drive the blade into the skull of the husk. With her other hand, she grabbed the poor creature and threw it over her shoulder. Her left foot snapped up and impacted the neck of yet another creature, snapping it instantly. Blood dripped from her shoulder as she kicked, elbowed, chopped and punched her way across the deck. More wounds appeared on her, from cuts on her face from the Husk's hands clawing at her to wounds on her calf where a husk had speared her.

Her breathing was very heavy; her hair was caked in gore and sweat. She brought her left arm up, ready for another strike, disregarding the fact that all of her limbs felt like lead weights. Alliana realized that there were no more Husks waiting for her. She closed her eyes at the pile of bodies before her, hardly believing that she was still alive. There had to be over a hundred husks scattered over the floor. She dropped to her hands and knees as her stomach revolted at the amount of energy that she had expended to fight to this point. As she wiped her mouth with the back of her hand, she noted that there was more then a little blood that she had expelled from her body. "No time…" She mumbled before standing up and entering a door way, noting a few marines running past. As she limped forward, she noted that she was rather near the beam.

Alliana broke into a run with the other marines, her body forced beyond its limits but some how finding the strength to keep moving. She picked up the rifle of a fallen marine, her hands bringing it up to fire from the hip as she ran, automatically adjusting for the recoil before she neared the beam when the sky lit up making her close her eyes from the brightness. She felt her body fly though the air. One word on her lips "Samantha…" she moaned as she impacted the ground.

*****Day 530 after invasion, In the relay system*****

"Commander, you better get to the Amory!" Vega called out to CIC over the intercom. "We have a problem down here."

Alliana let her hands let go of the rail that prevented her from stepping into the galaxy map "Traynor, hold…" she started but then noticed that the woman was not at her post, very not like her after a mission. She turned, running an armored hand though her hair, not having removed her armor from the last mission. She let her hand drop as she realized that she had brushed gore into her hair. After taking the lift to deck 5, she stepped out "Report James."

"It is Specialist Traynor Commander. It is like she's gone crazy. She's keeps trying on armor, as if she's trying to find the right fit. Between changes, she keeps kicking the lockers, punching them as well. The pistol next to her is empty. She unloaded it into one of the other lockers. I don…" He was cut off as Traynor let out a scream.

"FUCKING BASTARDS! I am going to fucking rip you limb from LIMB!"

Alliana took a deep breath as she held her hand up to Vega "I'll talk with her." She said before turning to walk deeper into the armory. She turned side ways after walking around a row of lockers as a chest piece of armor went flying past her.

"Samantha…" She said softly. When the locker in front of Traynor was punched, Alliana called her name louder.

"Commander." Samantha said finely as she turned to face the other woman. Her face was flushed and covered in sweat. The locker next to the one that was punched had been riddled with bullets.

Alliana stepped closer to the other woman, removing her gloves as she walked. "What happened Samantha?" she asked softly.

"Sanctuary." Samantha said as she slid down the locker, sitting on the floor. "EDI pulled the records of those who…" She faltered as she closed her eyes, tears starting to slide down her cheeks. Alliana sat next to her and wrapped her arms around her.

"What happened my love?" She asked.

"My parents were te…te…test subjects." She cried out. "They lived though the Collector attack on Horizon, we lived though the nightmare of being frozen and watching the collectors take everyone and yet…Cerberus kills them by making them sudo Husks, Banshees and Marauders…" She shook her head as she curled closer to Alliana. "I was there when the Collectors attacked. I helped keep my Parents alive but I still couldn't save them." She looked up into Alliana's face. "I want them to burn for what they did. I want them to die a horrible death. What happened to Lawson wasn't good enough. He died too quickly!" She said venom in her voice.

"Love, I understand that you are angry. I am angry." She said as she kissed the top of Samantha's head, drawing her arms tighter around the other woman. "I will make them pay for everything that they have done to you and me. Lawson has paid and The Illusive Man will pay. Ultimately, the ones that will pay are the Reapers and the lives that they warp into their twisted creatures. If it wasn't for them, none of this would have happened. No one would be dying, no Collectors, no Cerberus." She said, her hand softly stroking the other Woman's hair. Samantha's cries of pain slowly became louder as she mourned her parent's death. "Shhhh love….I'm here…" she cooed softly as she rocked the other woman.

The two of them sat on the floor for some time before Samantha's cries started to subside. Alliana shifted her body to slide her arms under Samantha's legs. She slowly stood up, supporting her lover by the legs and back with Traynor's arms around her neck. Shepard carried the other woman from the Armory and moved to enter the lift. "Commander?" Vega asked.

"Repair the damage she caused James. The war got to her. Not a word about anything you heard either." Alliana said.

"Aye aye Ma'am. Wouldn't dream of saying a thing." James said with a salute as Alliana entered the lift to her…no their quarters.

"I can't stand the thought of loosing you too Alliana." Samantha whispered as the lift started. "Every time you go on a mission, I am terrified that you won't come home to me."

"I always come home. There isn't a force in the Galaxy that won't stop me from coming home to you." Alliana said as she laid Samantha on the bed. She rested her hand on the cheek of her friend and lover, smiling softly at her.

"You better Alliana or you won't like what I do to you in the afterlife." Samantha said, her face smiling slightly.

"Yes Ma'am." Shepard said as she leaned down and softly kissed the other woman's lips.

****Day 589 after invasion above Earth, Sol System****

Shepard shook her head as she slowly picked herself off the ground. Her rifle was missing but there was a pistol. She gripped it with her right hand, limping forward. The sounds of combat seemed to fade from her as she closed in on the beam. Her hand reached up and touched her communicator. "EDI, I am entering the…" She coughed, spitting blood out. "beam. Monitor my audio."

"Yes Commander." EDI replied as Sheperd entered the beam.

Alliana blinked as she looked around the room she found herself in. Corpses were everywhere and she had no idea where she was. She slowly walked forward, seeing a door. After walking across a bridge, she saw a control panel. As she walked for it, the Illusive Man stepped in front of her.

"Get out of my way." Shepard demanded. "You Reaper indoctrinated piece of filth."

"Shepard, I can't say I am happy to see…" Before he could say any other word, Shepard snapped her hand up and fired two rounds. The second round was unnecessary as the first round impacted the Illusive Man's forehead. His head snapped back and he fell backwards, his head bouncing on the floor. "Fuck you asshole. That's for what you did to me and Samantha."

"Hackett, bring the rain." Shepard called out over her communicator. "The Citadel is ready." She said as she pressed the button to open the doors that would allow the Crucible to dock.

"Crucible docking now." Hackett called over the line less than two minutes later.

Shepard slid to the floor in front of the console, blood dripping down from her wounds. Her head started to drop as her eyes closed. "Shepard! Nothing's happening!" Hackett called out. "SHEPARD!" Alliana raised her head up. "ALLIANA!" Hackett screamed into her ear.

"I'll…check..." She gasped as she struggled to her feet. Pulling herself up onto the control console, she shook her head. "No...Nothing here...I'll...check the...power." She started to follow the only path, to a room. As she limped into the room, a child appeared. Clearly a construct as he was translucent, the child was the same as her dreams, as the boy that she could not save so long ago on Earth. "Stop the…"Alliana coughed, spitting blood on to the floor "Reapers." She commanded.

The boy turned to look at Shepard. "You must choose the fate of the Galaxy. The Reapers come to stop Artificial Intelligences from taking over the Galaxy. When the races of the Galaxy's become too powerful, the cycle restart's it self so other races may live. However, because you are here, I can no longer restart the cycle. No other Organic has ever made it this far. This proves that the Cycle must end. Alliana Shepard, you are to choose the way to end it."

Alliana snorted as the Citadel shook from another strike, causing the wounded Commander to loose her balance. She barely fought the fall, landing hard on her side. "A race of AI's harvesting every race in the Galaxy to stop us from failing to control our own AI's. We do not fear our own AI's. Even the Geth are working with us, no longer feared." Slowly she brought herself back to her feet.

"It is what must be done Shepard. The Geth turned on their creators. If organic life is not stopped, then, AI's will run rampart and destroy life in the Galaxy." The boy said.

Shepard shook her head. "It is part of life. We will find a way."

The child shook his head "You must choose. You have three options. One, you may choose to take control over the Reapers by fusing your life force into their own. Two, you may choose to wipe all Synthetic life from the Galaxy. This will include yourself Shepard as you are partly Synthetic. Or, the third option, merge Synthetic life with Organic life. All three options will result in the Mass Relays being destroyed. Choose wisely."

Alliana started to chuckle before coughing more blood up "That is rich. I chose none of the above. I want another option!"

"Working on it Commander." EDI said in her communicator.

"I have no way of knowing if I control the Reapers that they will not just win anyway. I feel that option is really a trick to stop me from stopping you. The second option is not an option as I cannot kill my friend EDI and all of the Geth out just to stop one race. I will not commit genocide. The last option frankly is also not an option as I will not play God with every race in the Galaxy. I also will not set every race back hundreds of years by removing their way of travel. Many races will never see their home worlds ever again. I choose another option." She stated.

"There is no time. To stop the Reapers, the Mass Relays must be used to send the beam though out the Galaxy. To stop the Cycle, they must be removed." The child said. "The time is now. Choose!" the child's voice became demanding and interlaced with several others.

"I choose that you take your Reapers and leave. The Galaxy has united to face your control method. All races working together to face a common goal, a common enemy. This includes Artificial Intelligences. Now leave. We can work with Synthetic life as the Geth and EDI proves." Alliana said.

"Commander, I have been going over the coding in the Citadel with the help of the Geth. We think we can control the Reapers with out loosing the Mass Relays." EDI said over the link. "However, I do not think we can complete this before Earth is lost completely."

"Give us the time we need to prove we can live in peace. Take the Reapers and go. We can do this." Alliana said, trying to buy the time they needed.

The child seemed to think for a few moments. "We will return. You will have your peace. When we return, oh yes we will return, we will complete this Cycle if you have not proven that you are right." The child started to fade from view.

"Wait!" Alliana called out

"No Shepard...the trial starts now. We will judge you when we return." The VI fades completely from view.

Alliana pressed her hand to her ear. "You got that EDI?" She asked, her voice almost a whisper from how weak she felt. She turned to start walking for a docking port.

"Yes Commander."

"Good. If I don..." she started to cough, crying out in pain. "If I don't make it, make sure ever...everyone knows. Stop the...the Reapers the nex..next time." She closed her eyes and tried to steady herself but she had little strength left in her frame.

"Commander?" EDI asked

Shepard sank to her knees. "I am sorry Samantha." She whispered. "I don't think I am going to come home." A tear splashed on the deck from her eyes. "I love you." She said as she fell forward, her body shutting down from the blood loss and the strain that she had put her body though.

"Commander, what ever you did worked! The Reapers are leaving!" Hackett came over the communicator. "Shepard! Respond!"

On the Normandy, EDI had patched Alliana to Traynor as she spoke her good byes. "JOKER!" Traynor screamed "Get us to the Citadel! Alliana needs us NOW!" She screamed as she ran for the control center.

"On it Traynor" Joker said as he moved his hands to move the ship.

"Stay alive….just stay alive Alliana…." Traynor prayed.

****Day 8 post Reaper Invasion, Sol System****

Shepard's eyes slowly opened. She heard soft beeps as her heart beat. She tilted her head slightly and felt the tubes in her throat. She flicked her eyes around the room and saw a dark haired woman resting her head on the bed, her hand in Alliana's own. She forced her hand to move and grip the other woman's own. A head shot up and Alliana saw the blood shot eyes of Samantha.

"Oh thank god!" She said, relief in her voice, lunging forward to wrap her arms around Shepard. "I thought I had lost you." Her voice breaking from the strength of the emotion in her. A doctor walked in, having been alerted that his patient had awoken.

"Ah Commander Shepard, good to see you awake. You have us quite the scare for a while. It was touch and go after the Reapers left." The doctor said. "You are on the Everest, in the Med Bay clearly. It will be a while before you can leave but I think we can remove that breathing tube now." The doctor slowly removed the tube down Alliana's throat. "I'll give the two of you a few moments." The doctor said before stepping out of the room.

"Thank you." She croaked. She looked at Samantha. "Wh..What's been goi...going on? Anderson? Joker? Ashley? Liara? Vega? Tali? Garrus? Did ever..everyone make it?" her voice barely a whisper.

"Shhh. It's alright Alliana." Traynor started to say, smiling softly at her lover. "Just get better." she said, though her eyes seemed to water slightly. "We'll talk more then."

"Tell me, who didn't make it." Alliana asked, almost begging in the whisper that she could muster.

Traynor took a deep breath as she sat up, knowing that Alliana would not let go of the issue until she knew. " Most of us on the Normandy came through with just a few bumps that were easily patched. Admiral Anderson was found near the beam. James lost a leg but, they are hopeful that they can give him a prosthetic soon while they regrow the leg. Ashley is currently MIA, presumed dead, Garrus is also MIA, however they are not hopeful. The area he was last seen in took the brunt of one of the last attacks." She gripped Alliana's hand as she reached up to stroke the other woman's cheek. " Liara, EDI, and the Geth are on the Citadel going though the computer, trying to find away to shut down the Reapers when they come back. Tali's suit was damaged badly. She is on a Quarian ship, fighting a massive infection. They are not hopeful at the moment that she..will live more than a month.." She placed her hands on Shepard's shoulder, stopping her from getting up. "You can't get up love. The doctors were surprised you were alive, much less walking to where they found you. Your pelvis was broken, fractures in your legs, cuts, burns, broken collar bone."

"I have to see Tali...Joker is the only other one left from when this started. I can't just... let her die without seeing her. Please let me say good bye. I've had to leave so many with no chance to say good bye." She said, tears forming in her eyes,

"Soon love. Soon." Samantha said.

The doctor walked back into the room. "I am sorry Samantha, but I'll need you to step out while we run a few tests and complete some treatments."

Samantha nodded to the doctor. "Alright Doc. I'll be back soon." She said as the doctor started to run scans on Alliana.

A week later, Shepard stood in her uniform, looking out of a viewport on the ship. She was grateful that she was able to convince Joker to smuggle in for her. "Shepard to the Med Bay" The call came out over the intercom. She shook her head before turning on her heal. She closed her eyes as pain shot though her leg and into her back. It reminded her that she was still alive. She needed to see her friend and that was more important to her then any pain.

She gritted her teeth as she entered the shuttle bay. As she stepped up to the flight officer, she told him that she needed a priority ride to the Quarian ship that had her friend. A few minutes later, she was on board the ship that Tali was on. "Take me to Tali'Zorah nar Normandy." she growled to the nearest Quarian that was on the flight deck. As she gripped the poor deck officer's chest. "Now Quarian!" She snarled. "She is of the Normandy, as the Captain of the Normandy, I have the right to know about her condition."

The Quarian "Yes Commander Shepard." He lead Shepard though the ship to their medical facilities. He pointed though a window "TaliZorah nar Normandy." he said. Shepard nodded and stepped up to the window.

"Doctor. How is she?" She asked the person that stepped up to her.

"She is doing better then she had been. We have kept her sedated to help her heal. We think that she will live but, we are not sure of her quality of life."

"What can I do to help her?"

"There is nothing more you can do. We will call you Commander Shepard if anything changes."

"You better. Call me when you wake her. I want to be here for her. She is of the Normandy."

"Yes Commander."

With that, she turned and walked away from her friend. She had several others to see before she was taken to the brig for stealing a shuttle. A short time later, she stepped off the shuttle on a frigate, heading for the Med Bay. She stepped in and saw James Vega laying on a bed. His eyes were closed with his face turned away from the door. Alliana sighed as she noted that his right leg was not there.

"Is that anyway to act when your Commanding Officer enters a room Vega?" She demanded as she stepped in. James snapped awake.

"Commander Shepard." He said. His face looked tired and pale. "Forgive me for not coming to attention but..."

"James, I do understand how you feel." She said.

"With all due respect, you've never lost a limb."

"Get over it James. I've been dead. Not mostly dead or nearly dead as you hear on the vids. I've been dead...deader than a door nail." She snapped as she drew up a chair, the back leaning on the bed's edge. "I should not even be moving around right now. I should be holed up in bed. So don't even give me that. I need you back on your feet as soon as you can. We have the next Reaper wave to contend with."

James looked at his Commander. "But you made them leave." He said.

"No James. I convinced them to give us a chance. A chance to recover and grow. They will be back. I do not know when, but they said we are on trial. I can only hope that we are ready for them. And in order to do that, I need you back on your feet to help train the Marines."

"Aye Aye Commander." James said, his face seeming to have lost some of the self pity that had formed on it when he awoke.

Shepard stood up. "Good. Now, I am sure Hackett is going spare looking for me. I kind of stole a shuttle to come see you." She said. "I must be getting back." She saluted James Vega. "Sergeant." she said before turning and leaving, going to face the music for her actions in the war.


End file.
